Acta Hortic. 1199. ISHS 2018. DOI 10.17660/ActaHortic.2018.1199.5 Proc. VIII Int. Olive Symposium Eds.: S. Perica et al. 27 Single nucleotide polymorphism (SNP) diversity in an olive germplasm collection F. Taranto 1,a , N. D’Agostino 2 , S. Pavan 3 , V. Fanelli 1 , V. di Rienzo 1 , W. Sabetta 1 , M.M. Miazzi 3 , S. Zelasco 4 , E. Perri 4 and C. Montemurro 1,3 1 SINAGRI S.r.l. - Spin off dell’Università degli Studi di Bari “Aldo Moro”, via Giovanni Amendola 165/A, 70126 Bari (BA), Italy; 2 Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Centro di Ricerca per l’Orticoltura, via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; 3 Università degli Studi di Bari “Aldo Moro”, via Giovanni Amendola 165/A, 70126 Bari (BA), Italy; 4 Centro di Ricerca per l’Olivicoltura e l’Industria, Contrada Lì Rocchi, 87036 Rende (CS), Italy. Abstract In contrast to other fruit crops, olive (Olea europaea) production is based mainly on traditional, locally selected cultivars. The world olive germplasm contains more than 2600 different cultivars, but olive genetic resources are poorly exploited and studied. Increasing our knowledge on olive tree genetics is a crucial step for breeding purposes and represents the future of olive growing. In the present work, we used the genotyping-by-sequencing (GBS) approach for genome-wide identification of single nucleotide polymorphisms (SNPs) to assess the level of genetic diversity in a collection of 78 olive cultivars. GBS analysis generated 37,792 high-quality SNPs, using an Olea europaea whole-genome sequence as reference. We were able to distinguish between SNPs located in intergenic regions (71.2%) and SNPs that overlap genes (28.8%), of which 2690 SNPs fell within annotated exons, affecting a total of 1302 genes. SNP markers developed by GBS and information on genetic diversity that emerged in this work will support genome-wide association mapping studies and breeding programs in olive. Keywords: Olea europaea, genotyping-by-sequencing, single nucleotide polymorphism, genetic diversity INTRODUCTION Based on estimates by the FAO, the world olive germplasm contains more than 2600 different varieties, including cultivars and wild trees. Genetic resources of this species are still poorly exploited (Muzzalupo et al., 2014), even though olive germplasm is characterized by a remarkable level of genetic variation that is reflected in a high degree of phenotypic plasticity. The availability of large germplasm collections including ancient olive genotypes is pivotal for the evaluation of genetic diversity and the detection of nucleotide polymorphisms associated with traits of interest. Until recently, olive genetic diversity was investigated mainly by using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers (Pasqualone et al., 2016; Boucheffa et al., 2017). Only a few studies have described the estimation of olive genetic diversity based on single nucleotide polymorphisms (SNPs) (Belaj et al., 2012; Kaya et al., 2013; Sabetta et al., 2013; Biton et al., 2015). The genotyping-by- sequencing (GBS) approach, based on next-generation sequencing (NGS) technologies, is now feasible for exploring olive genetic diversity on a genome-wide scale, since it provides a rapid, high-throughput and cost-effective tool for SNP discovery and genotyping (Elshire et al., 2011; Taranto et al., 2016a, b). Furthermore, the recent release to the public domain of an Olea europaea whole-genome sequence (Cruz et al., 2016) provides a unique opportunity for the implementation of NGS-based methods for assessing olive genetic diversity. As far as we a E‐mail: francesca.taranto@uniba.it